RetrogeneDB ID: retro_psin_36

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH206693.1:1238791..1239133(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSPSIG00000008882
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_psin_36
ATGCCCATGAAGGGCCGCTTCCCCATCTGCAGGACCCTGCAGTACTTGAGCCAGGGCAAGGTCATCTTCAAAAGCTCGGT
GAAGGTGCTGACTGAATTACAACACCCATGGGGAGCTGAGGAAGGGGGCCAGGAAATGTGTTTTTCAACATCCCCCAGAT
TCAGTACAAAACCCTTTGGGTGCAGATCATGATGTTTAGGAACATGACCCCTTTGCCATTCCTAAGGTTCTACTTAGATA
GTGGTGAGCAAGTCTTGTTTGATGTGGAAGGTAAAAAGCAACAAAGAGATAGTGGGTTAAAGCAAGGAAACACTACAAAA
AGAGGAGCAAGACGAAAAGAAG

Alignment

ORF - retro_psin_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 66.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPMKGRFPIRRTLQYLSQGEVVFKSSVKVLTVNYNSHGELSEGARKF-VFFNIPQIQYKNPWVQIMMFRN
          MPMKGRFPI.RTLQYLSQG.V.FKSSVKVLT......G...EG.....VFFNIPQIQYK..WVQIMMFRN
Retrocopy MPMKGRFPICRTLQYLSQGKVIFKSSVKVLTELQHPWG-AEEGGQEM<VFFNIPQIQYKTLWVQIMMFRN

Parental  MTPSPFLRFYLDSGEQVLVDVED-KSNREIVEHIKKILGKSEETLQK
          MTP.PFLRFYLDSGEQVL.DVE..KSN.EIV...K..L.K.E....K
Retrocopy MTPLPFLRFYLDSGEQVLFDVEG>KSNKEIVG*SKETLQKEEQDEKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_psin_36 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_36 was not experimentally validated.

Homology

Retrocopy orthology:

Pelodiscus sinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200,
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946, retro_mmul_874,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288, retro_opri_690, retro_opri_951,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36 ,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,